#[RUN: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Script/MS_profile_analysis.sh NextSeq1_10Cycles_S6_R1.fastq.gz CATGTAGTC TCTCT A A15 ]
# ========= [INFO] ==========
# Mut inCB: not accepter mutation in BC
# Mut inMS: 2
# ReadIn  : NextSeq1_10Cycles_S6_R1.fastq.gz
# seq_deb : CATGTAGTC
# seq_fin : TCTCT
# MS_seq : A
# excl : C,G,T
# nom  : A15
# log file: NextSeq1_10Cycles_S6_R1.A15.seq.log
# =============================
#
# condiGrep: CATG.AGTC.+AAA.+.CTCT|CATG.AGTC.+AAA.+T.TCT|CATG.AGTC.+AAA.+TC.CT|CATG.AGTC.+AAA.+TCT.T|CATG.AGTC.+AAA.+TCTC.|CATGT.GTC.+AAA.+.CTCT|CATGT.GTC.+AAA.+T.TCT|CATGT.GTC.+AAA.+TC.CT|CATGT.GTC.+AAA.+TCT.T|CATGT.GTC.+AAA.+TCTC.|CATGTA.TC.+AAA.+.CTCT|CATGTA.TC.+AAA.+T.TCT|CATGTA.TC.+AAA.+TC.CT|CATGTA.TC.+AAA.+TCT.T|CATGTA.TC.+AAA.+TCTC.|CATGTAG.C.+AAA.+.CTCT|CATGTAG.C.+AAA.+T.TCT|CATGTAG.C.+AAA.+TC.CT|CATGTAG.C.+AAA.+TCT.T|CATGTAG.C.+AAA.+TCTC.|CATGTAGT..+AAA.+.CTCT|CATGTAGT..+AAA.+T.TCT|CATGTAGT..+AAA.+TC.CT|CATGTAGT..+AAA.+TCT.T|CATGTAGT..+AAA.+TCTC.
# condiSet1: s/^.*CATG.AGTC//g;s/^.*CATGT.GTC//g;s/^.*CATGTA.TC//g;s/^.*CATGTAG.C//g;s/^.*CATGTAGT.//g
# condiSet2: s/.CTCT.*$//g;s/T.TCT.*$//g;s/TC.CT.*$//g;s/TCT.T.*$//g;s/TCTC..*$//g
# Pre-filtre ExactEnd: 21602 NextSeq1_10Cycles_S6_R1.A15.seq.exactEachEnd.MS
# Pre-filtre MutInEnd: 1604 NextSeq1_10Cycles_S6_R1.A15.seq.Max1MutEachEnd.MS
# [Creat: NextSeq1_10Cycles_S6_R1.A15.seq.MS.all ] 23180 lines.
#
#> SophieMS_GenotyperMS_unProfil.r NextSeq1_10Cycles_S6_R1.A15.seq.MS.all.nb A
#> SophieMS_GenotyperMS_unProfil_v2.r NextSeq1_10Cycles_S6_R1.A15.seq.exactEachEnd.MS.MS_noMut.nb NextSeq1_10Cycles_S6_R1.A15.seq.exactEachEnd.MS.MS_Mut.nb NextSeq1_10Cycles_S6_R1.A15.seq.Max1MutEachEnd.MS.MS_noMut.nb NextSeq1_10Cycles_S6_R1.A15.seq.Max1MutEachEnd.MS.MS_Mut.nb  A  NextSeq1_10Cycles_S6_R1.A15.seq.MS
# =============[ END ]===========
# [Creat: NextSeq1_10Cycles_S6_R1.A15.seq.MS.all.nb ]
# [Creat: NextSeq1_10Cycles_S6_R1.A15.seq.MS.all.profil.png ]
# [Creat: NextSeq1_10Cycles_S6_R1.A15.seq.MS.profil_v2.png ]
#
#nbRead	nbMSall	nb_EndnoMut_MSnoMut	nb_EndnoMut_MSMut	nb_EndMut_MSnoMut	nb_EndMut_MSMut
833492	23180	21454	140	1526	60
